Contacts of the helix formed by residues 521 - 527 (chain V) in PDB entry 1I84
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 521 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487V GLU* 3.5 42.2 - - + +
490V GLN* 3.6 23.8 - - + -
491V GLN* 2.6 26.9 + - + +
494V ASN* 4.0 10.3 - - - +
519V LEU* 4.5 6.3 - - + -
520V ASP* 1.3 91.1 - - - +
522V GLN* 1.3 65.2 + - - +
523V PRO* 3.1 6.3 - - - -
524V CYS* 3.0 12.7 + - - +
525V ILE* 2.9 18.6 + - + +
586V TYR* 3.8 24.2 - - + -
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Residues in contact with GLN 522 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488V LYS* 4.7 4.7 + - - +
491V GLN* 3.7 29.3 + - - +
495V HIS* 5.7 3.6 + - - -
520V ASP* 2.5 27.3 + - - +
521V LEU* 1.3 69.7 - - - +
523V PRO* 1.3 57.3 - - + +
525V ILE* 2.6 46.7 + - - +
526V GLU* 2.9 35.9 + - + +
529V GLU* 4.2 5.7 - - - +
675V ARG* 6.2 0.2 - - - +
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Residues in contact with PRO 523 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520V ASP* 3.0 17.9 - - + +
521V LEU* 4.0 5.6 - - - -
522V GLN* 1.3 89.2 - - + +
524V CYS* 1.3 55.2 + - - +
525V ILE 2.5 13.7 + - - -
526V GLU* 2.7 23.8 + - + +
527V LEU 3.1 9.2 + - - -
566V HIS* 3.8 19.2 + - + -
567V ALA* 6.2 1.8 - - + -
568V LYS* 4.6 9.6 - - + +
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Residues in contact with CYS 524 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487V GLU* 3.3 29.0 - - - +
521V LEU* 3.0 11.3 + - + +
523V PRO* 1.3 76.3 - - - +
525V ILE* 1.3 56.6 + - - +
527V LEU* 4.2 6.7 - - - +
528V ILE* 3.2 19.5 - - - +
568V LYS* 3.7 28.1 - - + +
583V ILE* 4.9 7.0 - - - -
584V LEU 3.4 24.7 - - - -
585V HIS* 3.7 21.5 - - - -
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Residues in contact with ILE 525 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484V TYR* 3.5 28.9 - - + -
487V GLU* 4.9 7.9 - - + +
488V LYS* 4.2 23.1 - - + +
491V GLN* 4.3 16.6 - - + -
521V LEU* 2.9 22.7 - - + +
522V GLN* 2.6 39.6 + - - +
523V PRO 2.5 5.3 + - - -
524V CYS* 1.3 71.6 - - - +
526V GLU* 1.3 57.6 + - - +
527V LEU 3.2 1.6 - - - -
528V ILE* 2.9 5.5 + - - +
529V GLU* 2.4 57.6 + - - +
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Residues in contact with GLU 526 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522V GLN* 3.2 36.4 - - + +
523V PRO* 2.7 15.9 + - + +
525V ILE* 1.3 76.4 - - - +
527V LEU* 1.3 53.4 + - - +
528V ILE 2.6 11.6 + - - -
529V GLU* 3.1 24.5 + - - +
530V ARG* 3.2 54.1 + - + +
534V PRO 4.9 0.8 - - - +
535V PRO 4.4 1.5 - - - +
536V GLY* 3.5 8.3 + - - -
566V HIS* 5.0 3.1 - - - +
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Residues in contact with LEU 527 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523V PRO 3.1 5.3 + - - +
524V CYS 4.2 8.7 - - - +
525V ILE 3.2 0.2 - - - -
526V GLU* 1.3 76.6 - - - +
528V ILE* 1.3 56.1 - - + +
535V PRO 4.9 0.2 - - - -
536V GLY* 3.5 2.3 - - - -
537V VAL* 2.8 38.5 + - + +
563V GLN* 3.6 18.7 - - + +
566V HIS* 3.1 49.2 + - + +
568V LYS* 3.3 33.0 - - + +
569V PHE* 3.5 12.3 - - + +
583V ILE* 3.5 18.4 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il